Category Archives: OS

Naga101: A Guide to Getting Started with (OPIG) Slurm Servers

Over the past months, I’ve been working with a few new members of OPIG, which left me answering (and asking) lots of questions about working with Slurm. In this blog post, I will try to cover key, practical basics to interacting with servers that are set up on Slurm.

Over the past months, I’ve been working with a few new members of OPIG, which left me answering (and asking) lots of questions about working with Slurm. In this blog post, I will try to cover key, practical basics to interacting with servers that are set up on Slurm.

Slurm is a workload manager or job scheduler for Linux, meaning that it helps with allocating resources (eg CPUs and GPUs) on a server to users’ jobs.

To note, all of the commands and files shown here are run from a so-called ‘head’ node, from which you access Slurm servers.

1. Entering an interactive session

Unlike many other servers, you cannot access a Slurm server via ‘ssh’. Instead, you can enter an interactive (or ‘debug’) session – which, in OPIG, is limited to 30 minutes – via the srun command. This is incredibly useful for copying files, setting up environments and checking that your code runs.

srun -p servername-debug --pty --nodes=1 --ntasks-per-node=1 -t 00:30:00 --wait=0 /bin/bash

2. Submitting jobs

While the srun command is easy and helpful, many of the jobs we want to run on a server will take longer than the debug queue time limit. You can submit a job, which can then run for a longer (although typically still capped) time but is not interactive, via sbatch.

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Dealing with multiple compilers

I don’t know you, but when I am compiling a complicated program and everything goes straightforward I feel a mixture of joy and surprise. Let’s face it, compiling can be quite frustrating, and if you need to compile something relatively old, chances are that you will spend hours and hours trying to understand the compiler error messages.

Several such compiler errors, that in many cases can be quite convoluted, tell you that your program requires an older version, so you first need to install it. I am going to assume that you have sudo rights, otherwise, we will be playing the game of compiling a compiler, something that I recommend you to do at least and at most once in your life.

In common Linux distributions like Ubuntu, installing an older compiler is as easy as using apt or yum:

#Ubuntu
$ sudo apt install build-essential
$ sudo apt install gcc-7 g++-7
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Linux Horror stories vol II: Automatic drivers update

As promised, I will tell you about another Linux Horror Story: The Nvidia driver automatic update that breaks your machine. This is a recurrent problem that I have suffered so many times that I tend to disable all Nvidia updates just to avoid it. Unfortunately, I forgot to do so on my new laptop, so it happened once more. 

It all started when I tried to connect my dual monitor to my laptop, as I have been doing for the last 8 months. But the SO did not recognize the monitor. After unplugging and plugging my monitor a few times and rebooting my machine several times, I started thinking that it may be a drivers-related problem, so I just executed the command nvidia-smi to check if the GPU drivers were working. A familiar error message confirmed my fears: 

NVIDIA-SMI has failed because it couldn’t communicate with the Nvidia driver. 

 Make sure that the latest NVIDIA driver is installed and running.

If you are lucky enough, this is a consequence of the driver update and rebooting the machine will make it work again. Unfortunately, it was not my case, so I started the process of uninstalling and reinstalling the drivers. To do so, in an Ubuntu machine, you only need to use the following two commands.

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How to Install Open Source PyMOL on Windows 10

It is possible to get an installer for the crystallographer’s favourite molecular visualization tool for Windows machines, that is if you are willing to pay a fee. Fortunately, Christoph Gohlke has made available free, pre-compiled Windows versions of the latest PyMOL software, along with all of it’s requirements, it’s just not particularly straightforward to install. The PyMOLWiki offers a three-step guide on how to do this and I will break it down to make it somewhat clearer.

1. Install the latest version of Python 3 for Windows

Download the Windows Installer (x-bit) for Python 3 from their website, x being your Windows architecture – 32 or 64.

Then, follow the instructions on how to install it. You can check if it has installed by running the following in PowerShell:

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